Contacts of the strand formed by residues 665 - 668 (chain A) in PDB entry 6BM0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 665 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A VAL* 3.7 27.1 - - + -
658A ILE 3.4 3.4 - - - +
659A MET* 4.3 5.8 - - + -
663A GLY 3.8 8.5 + - - +
664A HIS* 1.3 81.1 - - - +
666A THR* 1.3 65.5 + - - +
686A LYS* 3.4 17.1 - - - +
687A PRO* 3.3 35.5 - - + +
689A LEU* 4.9 7.4 - - + -
691A HIS* 5.1 5.0 - - + +
695A VAL* 4.4 18.2 - - + -
698A LEU* 4.2 18.6 - - + -
787A LEU* 4.8 5.8 - - + -
802A TRP* 5.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A VAL* 4.4 18.1 - - + +
656A VAL 3.9 0.6 - - - +
657A VAL* 3.3 2.4 - - - +
658A ILE* 2.6 65.6 + - - +
664A HIS* 5.5 4.5 - - + -
665A VAL* 1.3 80.9 - - - +
667A MET* 1.3 58.6 + - - +
668A PHE* 5.2 2.6 - - - -
684A LEU* 3.8 24.9 - - + -
686A LYS* 4.4 17.5 - - + +
687A PRO* 4.1 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A TYR* 3.7 31.6 - - + -
656A VAL 3.2 2.9 - - - -
657A VAL* 3.7 19.3 - - + +
666A THR* 1.3 75.2 - - - +
668A PHE* 1.3 80.5 + - - +
669A LEU* 5.6 1.6 - - + -
684A LEU* 3.8 0.3 - - - +
685A HIS* 2.8 73.4 + - + +
687A PRO* 4.2 7.4 - - + +
799A LEU* 3.7 15.9 - - - +
800A PRO 5.1 4.3 - - - +
802A TRP* 3.5 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ILE* 2.5 57.2 - - + -
638A ILE* 3.9 13.2 - - + -
640A VAL* 4.8 6.7 - - + -
655A TYR* 3.4 5.4 - - - -
656A VAL* 2.4 54.1 + - + +
658A ILE* 3.8 15.5 - - + -
666A THR* 5.2 3.8 - - - -
667A MET* 1.3 89.4 - - - +
669A LEU* 1.3 64.9 + - - +
682A LEU* 4.0 21.5 - - + -
683A ALA 3.2 15.9 - - - +
684A LEU* 3.6 34.8 - - + -
685A HIS* 5.7 0.7 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il